Modelling the DNA double helix
using recycled materials
Dionisios Karounias, Evanthia
Papanikolaou and Athanasios Psarreas,
from Greece, describe their innovative model
of the DNA double helix – using empty
bottles and cans!
This project to construct a 3D model of a
DNA molecule, using everyday materials,
stimulated the students’ interest,
encouraged teamwork, dexterity and the
investigation of the properties of materials,
and allowed the students to express their
own opinions and solve problems. More
specifically, students learned the basic
structural elements of DNA and their 3D
molecular organisation.
Model of the DNA helix
Molecular structure of DNA
The basic unit of DNA is the nucleotide,
consisting of a phosphate group, a sugar
molecule (deoxyribose) and one of four
nucleobases (also known as bases): adenine
(A), thymine (T), guanine (G) or cytosine
(C).
The DNA molecule consists of successive
nucleotides arranged in a double helix – a
spiral ladder – the sides of which are formed
from sugar and phosphate groups, with each
A nucleotide
step consisting of a pair of bases. The base
pairs are formed from complementary
nucleotides: adenine pairs with thymine,
while guanine pairs with cytosine.
A model nucleotide
The model
Each of the three constituents of the nucleotide were represented with
3D objects (see Table 1) which were connected to form a double helix
with ten steps (base pairs). See below.
DNA molecule
Phosphate group
Deoxyribose molecule
Base
Model
Coca Cola® can
Sprite® can
Plastic bottle
Table 1: DNA molecular components and the corresponding model materials
Materials
Recycled materials
Our choice of materials reflected their abundance in the school
recycling bins.
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20 aluminium Coca Cola® cans
20 aluminium Sprite® cans
20 plastic Coca Cola bottles (500 ml)
60 red caps from Coca Cola bottles
10 plastic Fanta® bottles (500 ml)
20 orange caps from Fanta bottles
a thin piece of paper or plastic, approximately 1 m long.
Additional materials
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6 m thin rope
20 plastic drinking straws
20 nuts and thin double-threaded bolts
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4 sheets of coloured confectionery cellophane (blue, green, red
and yellow).
Tools
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Scalpel or sharp knife for cutting the plastic bottles
Thick nail for the making holes in plastic and aluminium
Small pliers
Stapler
Two pieces of thin telephone cable, about 40 cm long, for
passing the rope through the straws.
Method
First, each of the three nucleotide constituents (deoxyribose,
phosphate and base) are modelled, reflecting the geometry of the
molecule as far as possible. Next, the components are assembled to
form nucleotides and the DNA helix is constructed.
Puncture the aluminium cans and the bottle caps with the same nail.
Heating the nail will enable the caps to be more easily pierced. Choose
a suitable thickness of nail to enable the plastic drinking straws to pass
through the holes and fit firmly, creating a stable link between the
structural elements.
Deoxyribose
Deoxyribose is modelled with a Sprite can
with three red bottle caps attached,
representing the carbon atoms at the 1’, 3’
and 5’ positions. An orange bottle cap at
position 3’ represents the hydroxide that will
be connected to the next nucleotide.
Deoxyribose
1. Puncture the can in positions 1’, 3’ and
5’, as shown below.
2. Puncture four bottle caps (three red
and one orange) in the centre.
3. Using a nut and bolt, attach a red cap
firmly in position 1’ so that a bottle can
be screwed on.
4. Firmly attach two caps, one red and
one orange, to one end of a straw
(first the red, then the orange).
5. Pass the straw through the can, using
holes 3’ and 5’.
6. Fix the can to the straw, threading
another red cap to the side of the can
in position 5’. The final result can be
seen to the left.
Phosphate group
Phosphate and
deoxyribose
Using the same nail, puncture the centre of
the Coca Cola can base, which represents
the phosphate group. Thread the straw
attached to the Sprite can (deoxyribose)
through the Coca Cola can (phosphate
group), with the top of the Coca Cola can
closest to the Sprite can. The phosphate
group is now attached to the deoxyribose in
position 5’ (see left).
The straw connects the two cans, and also
makes it easy to pass the thin rope through
both cans, connecting the nucleotides into a
molecule chain (see below). For this reason,
it is important not to bend the straw. To
maintain the correct scale between the
molecule and the model, the distance from
the base of the Coca Cola can to the orange
cap should be 23 cm.
Complementary base pairs
Next, plastic bottles representing the bases are modelled so that they
can only be connected to their complementary base (adenine to
thymine, and guanine to cytosine).
To construct two complementary base pairs, cut two Fanta bottles and
three Coca Cola bottles in cross-section, using the scalpel and scissors.
Take care!
1. Remove the base of two Coca Cola bottles (incision c below)
2. From the third Coca Cola bottle, remove
o the neck, cutting 10 cm below the mouth (incision a) and
o the lower part of the bottle, cutting 4 cm above the base
(incision b).
3. Using scissors, make five to six incisions, 2 cm long, in the neck
and the base of the third Coca Cola bottle. These can then open
to allow other bottles in (see below).
4. Using these building blocks and the coloured cellophane, the
structural elements that represent the bases can be created.
Constructing the bases
Thymine (T)
Place green cellophane in a Coca Cola bottle without a base.
Adenine (A)
To the base of a Fanta bottle, attach the neck of a Coca Cola bottle.
Place blue cellophane inside both parts.
Thymine (T), represented by the colour green, is connected by two
hydrogen bonds to adenine (A), represented by the colour blue. To
model this, push the blue neck firmly into the green bottle without the
base.
Guanine (G)
Place red cellophane in a Fanta bottle.
Cytosine (C)
Place yellow cellophane in a Coca Cola bottle without a base. Firmly
attach the base of another Coca Cola bottle, upside down.
Guanine (G), represented by the colour red, is connected by three
hydrogen bonds to cytosine (C), represented by the colour yellow. To
model this, open the base of the yellow bottle (cytosine) along the
incisions to allow the base of the red bottle (guanine) to enter and lock
firmly.
For symmetry and the scale of the model, the two pairs of linked
complementary bases should be 42 cm long. Each coloured bottle is
screwed into the bottle cap (carbon) at position 1’ of a deoxyribose
molecule, forming four different nucleotides (see below).
Complementary bases
This representation of the hydrogen bonds enables the easy
connection and detachment of complementary bases. This, in turn,
facilitates not only the separation of the DNA strands but also the
change in position of bases for teaching purposes.
Complementary base pairing
Constructing the DNA molecule
Having constructed 20 nucleotides, we can build a double helix with 10
steps – two strands of 10 nucleotides each. Because the distance from
the end of the Coca Cola can (phosphate group) to the orange cap
(hydroxide linked with the next phosphate group) is 23 cm, the strand
of 10 nucleotides will be 2.3 m long.
Attach the telephone cable to approximately 3 m of the thin rope and
use the stiff cable to pass the rope through the straws of the
nucleotides to form two strands of molecules, which are hung vertically
2 m high and 65 cm apart. The two strands of the DNA molecule are
read in the direction 5’ to 3’ and are anti-parallel. In the model, the
direction in which we read the word Coca Cola coincides with the
direction 5’ to 3’. Thus, in one of the strands, the words Coca Cola can
be read from top to bottom and in the other strand, from bottom to
top. Our model DNA strands are thus also anti-parallel.
We must also make sure that the bases on one strand are
complementary to those on the opposite strand. Adenine should be
opposite thymine and cytosine opposite guanine.
If these criteria have been met, tie a paper roll at the end of each
strand so that a thin bar can be passed through the roll and used to
twist the linked strands clockwise, 360 degrees (see below).
Diameter
Helix step
Helix length
Helix length: diameter
Helix step: diameter
DNA molecule
2 nm
3.4 nm
7.14 nm
3.57
1.7
Model
0.65 m
1.1 m
2.30 m
3.53
1.7
Table 2: Sizes and proportions of a DNA molecule and the model
The model represents a DNA molecule at a scale of 320 000 000:1,
that is, 320 million times bigger than it really is. If we tried to
represent an entire human DNA molecule with our model, we would
need a double helix 640 000 km long, capable of wrapping around
Earth’s equator 16 times.
Using the model in class
The model was constructed and used in
three phases over one to two weeks.
Phase 1: Constructing the model
Students aged 14 followed the construction
directions with interest and were involved in
resolving practical problems.
Phase 2: Representing a DNA molecule
In the appropriate unit of their biology
course, students aged 15 were given a
worksheet where they recognised and
matched the prepared structural materials of
the model with those of the DNA molecule as Hanging the helix
illustrated in their textbook. They composed
and twisted the double chain of the model.
They asked a lot of questions and had an
intense and interesting discussion.
Phase 3: Copying a DNA molecule
In their free time and as a theatre game, the
same 15-year-old students pretended to be
suitable enzymes and, with the help of the
model, performed the following steps:
1. Splitting hydrogen bonds between the
complementary bases, from the top of
the molecule until the sixth base
(bottle) pair on the model (enzyme:
DNA helicase).
2. Separating the two strands.
3. Beginning to create daughter strands
complementary to the parental strand
(DNA polymerase).
4. Splitting the rest of the hydrogen
bonds.
5. Creating daughter strands
complementary to the parental strand
(DNA polymerase).
6. Checking for possible errors and
correcting them if necessary.
Twisting the helix